ArticleProceedings of the National Academy of Sciences of the United States of America2008
Insights into protein flexibility: The relationship between normal modes and conformational change upon protein-protein docking.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 85 papers.
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Who cites it
85 citing papers in PubMed.
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- Extended Sampling of Macromolecular Conformations from Uniformly Distributed Points on Multidimensional Normal Mode Hyperspheres.Journal of chemical theory and computation · 2024Article
- Dynamic allostery in the peptide/MHC complex enables TCR neoantigen selectivity.Research square · 2024Article
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- Critical Assessment of Methods for Predicting the 3D Structure of Proteins and Protein Complexes.Annual review of biophysics · 2023Review
- Electrospray ion beam deposition plus low-energy electron holography as a tool for imaging individual biomolecules.Essays in biochemistry · 2023Article
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- Structure and activity of a thermally stable mutant of Acanthamoeba actophorin.Acta crystallographica. Section F, Structural biology communications · 2022Article
- Low-energy electron holography imaging of conformational variability of single-antibody molecules from electrospray ion beam deposition.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- In silico Design of a Vaccine Candidate for SAR S-CoV-2 Based on Multiple T-cell and B-cell Epitopes.Archives of Razi Institute · 2021Article
- Low-Frequency Harmonic Perturbations Drive Protein Conformational Changes.International journal of molecular sciences · 2021Article
- DynamicsProceedings of the National Academy of Sciences of the United States of America · 2021Article
- Drug design by machine-trained elastic networks: predicting Ser/Thr-protein kinase inhibitors' activities.Molecular diversity · 2021Article
- Article
- Rewards of divergence in sequences, 3-D structures and dynamics of yeast and human spliceosome SF3b complexes.Current research in structural biology · 2021Article
25 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Understanding protein interactions has broad implications for the mechanism of recognition, protein design, and assigning putative functions to uncharacterized proteins. Studying protein flexibility is a key component in the challenge of describing protein interactions. In this work, we characterize the observed conformational change for a set of 20 proteins that undergo large conformational change upon association (>2 A Calpha RMSD) and ask what features of the motion are successfully reproduced by the normal modes of the system. We demonstrate that normal modes can be used to identify mobile regions and, in some proteins, to reproduce the direction of conformational change. In 35% of the proteins studied, a single low-frequency normal mode was found that describes well the direction of the observed conformational change. Finally, we find that for a set of 134 proteins from a docking benchmark that the characteristic frequencies of normal modes can be used to predict reliably the extent of observed conformational change. We discuss the implications of the results for the mechanics of protein recognition.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.